kopardev commented 1 year ago

Create docker for it and add it to the pipeline!

kopardev commented 1 year ago

Docker nciccbr/ccrgb_fusioncatcher:v1.0 is based off of conda installation of fusioncatcher

kopardev commented 1 year ago

Docker nciccbr/ccrgb_fusioncatcher:v2.0 is based off direct installation of fusioncatcher using bootstrap.py script (as recommended here)

kopardev commented 1 year ago

Required database to be either

[x] downloaded ... downloaded v102
[x] built ... built v108 on local macbook

kopardev commented 1 year ago

v102 and v108 pushed to s3 along with a local copy. s3 will be used for AGC execution and local copy under the khanlab mount will be used for biowulf execution.

kopardev commented 1 year ago

Ran into this error.

kopardev commented 1 year ago

Ran into this error.

Fixed by replacing fusioncatcher in the command with fusioncatcher.py. It was unable to find the config file which exists in the docker in the etc folder.

kopardev commented 1 year ago

Biowulf working version available in commit

kopardev commented 1 year ago

fusioncatcher requires a "database" to run ... it can either be:

downloaded --> this is v102
```
#!/usr/bin/env bash
```

FusionCatcher v1.33 uses Human Ensembl v102

echo "Downloading Human Ensembl v102 database to ${FC_DB_PATH}/current/..."

Direct download:

cd ${FC_DB_PATH}

rm -rf human.tar.gz.

wget --no-check-certificate http://sourceforge.net/projects/fusioncatcher/files/data/human_v102.tar.gz.aa -O human_v102.tar.gz.aa wget --no-check-certificate http://sourceforge.net/projects/fusioncatcher/files/data/human_v102.tar.gz.ab -O human_v102.tar.gz.ab wget --no-check-certificate http://sourceforge.net/projects/fusioncatcher/files/data/human_v102.tar.gz.ac -O human_v102.tar.gz.ac wget --no-check-certificate http://sourceforge.net/projects/fusioncatcher/files/data/human_v102.tar.gz.ad -O human_v102.tar.gz.ad

cat human_v102.tar.gz.aa human_v102.tar.gz.ab human_v102.tar.gz.ac human_v102.tar.gz.ad > human_v102.tar.gz rm -f human_v102.tar.gz.aa human_v102.tar.gz.ab human_v102.tar.gz.ac human_v102.tar.gz.ad tar xzvf human_v102.tar.gz rm -f human_v102.tar.gz

echo "Human Ensembl v102 database is downloaded."

exit 0


- built --> this is v108

CCRGeneticsBranch / Oncogenomics_NF_WF

Fusioncatcher #2

FusionCatcher v1.33 uses Human Ensembl v102

echo "Downloading Human Ensembl v102 database to ${FC_DB_PATH}/current/..."

Direct download:

cd ${FC_DB_PATH}